Why we love basic research

Brandeis PhD students Jonathan Napoline (Graduate Program in Chemistry, Thomas lab) and Sara Haddad (Graduate Program in Neuroscience, Marder lab) tell PBS NewsHour why they’re excited about basic research



Rectifying electrical synapses in pattern-generating circuits

by Gabrielle Gutierrez

Rectifying electrical synapses are more interesting than they might seem at first. Our recent study finds that they have the potential to allow a circuit to control how robust the circuit output is to modulation of synaptic strength.

Gap junctions allow neurons to communicate quickly by serving as a direct conduit of electrical signals. Non-rectifying gap junctions probably come to mind first for most neuroscientists when they think about electrical synapses, since they are the idealized textbook variety. The electrical current that passes through the non-rectifying type of gap junction is simply a function of the voltage difference between the coupled neurons. However, this is only the case when the two hemi-channels that form a gap junction pore have the same voltage-dependencies.

Schematic shows that neurons can express diverse gap junction subunits (top left). Rectifying gap junction conductance is a function voltage difference between two neurons (top right). Bottom panel illustrates how coupled neuron output depends on the polarity of the rectifying electrical synapse and the intrinsic properties of the coupled neurons.

Schematic shows that neurons can express diverse gap junction subunits (top left). Rectifying gap junction conductance is a function voltage difference between two neurons (top right). Bottom panel illustrates how coupled neuron output depends on the polarity of the rectifying electrical synapse and the intrinsic properties of the coupled neurons.

We know from past electrophysiology studies that a single neuron can express a diverse set of gap junction hemi-channels, enabling it to form similarly diverse gap junction channels with another neuron. This could result in rectifying electrical synapses in which current flows asymmetrically between neurons so that current flow can either be permitted or restricted depending on whether the current is positive or negative. What we didn’t know were the consequences of electrical synapse rectification for a pattern-generating circuit of competing oscillators. Our recently published study in J. Neuroscience addressed this question and led us to conclude that rectifying electrical synapses can change how a neuronal circuit responds to modulation of its synapses – including its chemical synapses. Although we used a computational model for our study, our results indicate that rectifying electrical synapses in biological networks can be an important component in neuronal circuits that produce rhythmic patterns, such as those found in motor systems.

Gabrielle Gutierrez obtained her PhD in Neuroscience from Brandeis earlier this year, and is currently doing a postdoc with Sophie Deneuve at the Ecole Normale Superieure in Paris

Gutierrez GJ, Marder E. Rectifying electrical synapses can affect the influence of synaptic modulation on output pattern robustness. J Neurosci. 2013;33(32):13238-48.

IGERT Summer Institute

 The Brandeis IGERT program is hosting its first summer institute starting Wednesday, July 31 and running weekdays through Friday, August 9. This will be a series of lectures by experts inside and outside of Brandeis, together with some student seminars, aimed at graduate students across the sciences, especially (but not exclusively!) those doing theoretical work.

The lectures will run from 9:30-4 every day, with coffee at 9am, and ample time between lectures for questions and conversations.  They will be held in room 055 of the Lemberg Academic Center (note that Domenic’s will be open at that time, so lunch is available nearby).  Those interested in attending should RSVP to Tony Bottaro (bottaro@brandeis.edu) so that we can get a head count for coffee.

The lecturers are:

Parongama Sen (University of Calcutta, Kolkata, India), lecturing on applications of statistical physics to social science problems.
Henry Cohn (Microsoft Research, New England), lecturing on symmetry and optimization.
Ben Allen (Emmanuel College and Harvard), lecturing on evolutionary dynamics
Paul Miller (Brandeis), lecturing on aspects of theoretical neuroscience.
Blake LeBaron (Brandeis), lecturing on empirical puzzles in financial data, and applications of agent-based modeling.
Albion Lawrence (Brandeis), lecturing on fiber bundles (“gauge theory”) and their applications to deformable bodies (falling cats, swimming bacteria).

In addition, we will have seminars by IGERT students:

Sumantra Sarkar
Blake Stacey
Daniel Goldstein

and a schedule can be found on this webpage:


Making new synapses with Sema4D

There are two main types of synaptic connections in the mammalian brain: excitatory glutamatergic synapses and inhibitory GABAergic synapses. The balance between excitatory and inhibitory inputs a neuron receives regulates the overall activity of neuronal networks; disruptions to this balance can cause epilepsy.

A new paper in J. Neuroscience from the Paradis lab shows that treatment of cultured neurons with the extracellular domain of the protein Sema4D causes a rapid increase (i.e. within 30 minutes) in the density of functional GABAergic synapses. Further, addition of Sema4D to neurons drives GABAergic synapse formation through a previously unappreciated mechanism: the splitting of pre-existing assemblies of the Gephyrin scaffolding protein. To our knowledge this is the fastest demonstration of synapse formation reported thus far and has significant implications for our understanding of the mechanisms of GABAergic synapse formation.

Screen Shot 2013-05-26 at 5.03.05 PMWhile the underlying mechanism of epileptogenesis is largely unknown, recurrent seizures emerge when there is an increase in network activity. One possible therapeutic treatment would be to restore normal network activity by increasing network inhibition. In an in vitro model of epilepsy, acute treatment with the protein Sema4D rapidly silences neuronal hyperexcitability, suggesting a possible use of Sema4D as a disease-modifying treatment for epilepsy.

Lead authors on the paper were Marissa Kuzirian, a grad student in the Neuroscience Ph.D. program, and Anna Moore, a Brandeis Neuroscience postdoctoral fellow.

NSAID gels and COX-2 selectivity in topical pain killers

Research from Bing Xu’s lab, published in November in Journal of the American Chemical Society, has recently been featured in C&E News. The Xu lab researchers, including Chemistry grad students Jiayang Li, Yi Kuang, Yuan Gao, Xuewen Du and Junfeng Shi, synthesized hydrogels by synthetically coupling small D-amino acid peptides to naproxen (a non-steroidal antiinflammatory drug – NSAID). This was done with the idea of forming gels that can be used for topical pain treatment.

Studies on the compounds formed showed that not only are gels formed, but the D-peptide conjugates of naproxen showed better selectivity towards COX-2 (the therapeutic target) compared to COX-1 (a source of side effects) than naproxen alone or an L-peptide conjugate. Clinical applications are still far away, but this finding opens exciting new avenues for research.

Li J, Kuang Y, Gao Y, Du X, Shi J, Xu B. d-Amino Acids Boost the Selectivity and Confer Supramolecular Hydrogels of a Nonsteroidal Anti-Inflammatory Drug (NSAID). J Am Chem Soc. 2012.

Damaged DNA and self-eating (autophagy) in budding yeast.

Chromosome double-strand breaks (DSBs) threaten the integrity of the genome. Cells respond to DSBs by activating the DNA damage checkpoint that blocks cells prior to mitosis, allowing more time for the repair of damaged DNA. When the DSB can be repaired, the cell cycle checkpoint is turned off so that cells can resume cell cycle progression, a process termed recovery. If the DSB remains unrepaired, G2/M arrest persists for a long time but eventually cells adapt and – despite the persistent DNA damage – complete mitosis and divide. Much of our understanding of the DNA damage response has come from the study of the budding yeast Saccharomyces cerevisiae, where it is possible to create DSB damage synchronously in all cells of the population. This can be accomplished either by uncapping telomeres, exposing their normally protected ends or by creating a single, defined DSB by inducing the site-specific HO endonuclease. From such studies, it was possible to identify a highly evolutionarily conserved DNA damage sensing and signaling cascade that is initiated by Mec1, the yeast homolog of mammalian ATR protein kinase (reviewed in Ref. (1)). Yeast genetic approaches revealed a number of adaptation-defective mutants, a subset of which also are recovery-defective. Previous studies also demonstrated that triggering the DNA damage checkpoint affects not only mitosis and the efficiency of DNA repair within the nucleus; it also affects cytoplasmic responses (2, 3). In a new paper from the Haber lab published in PNAS, we uncovered mutations in the Golgi-Associated Retrograde Protein (GARP) complex that are adaptation-defective. We show that the defect in these mutants can be mimicked by activating the cytoplasm-to-vacuole (CVT) pathway of autophagy that prevents the nuclear accumulation of separase, Esp1, in the nucleus, thus preventing the cells both adapting and recovering from DSB damage.

In budding yeast, a single unrepaired double-strand break (DSB) triggers the Mec1-dependent cell cycle arrest prior to anaphase for 12-15 before they adapt. Adaptation is accompanied by the loss of hyperphosphorylation of Rad53, yeast’s Chk2 homolog.  Rad53 remains phosphorylated in a number of adaptation-defective mutations, including deletion of the two PP2C phosphatases, ptc2ptc3D, that normally dephosphorylate Rad53.  Adaptation is also blocked by ablating a number of proteins with diverse roles in DSB repair, including srs2D, rdh54D as well as by a mutation in yeast’s polo kinase cdc5-ad.

In our paper, we find that hyperactivation of the cytoplasm-to-vacuole (CVT) autophagy pathway causes the permanent G2/M arrest of cells with a single DSB that is reflected in the nuclear exclusion of both separase, Esp1, and its chaperone/inhibitor, securin, Pds1(See figure).  Autophagy in response to DNA damage can be induced in three different ways: (1) by deleting members of the Golgi-Associated Retrograde Protein complex (GARP) such as vps51D; (2) by adding rapamycin; or (3) by overexpressing a dominant-negative ATG13-8SA mutation.  The permanent checkpoint-mediated arrest in any of these three conditions can be overcome in three ways: (1) by blocking autophagy with mutations such as atg1D, atg5D or atg11D; (2) by deleting the vacuolar protease Prb1 or its activator, Pep4; or (3) by driving Esp1 into the nucleus with a SV40 nuclear localization signal.  In contrast, these same alterations fail to suppress the adaptation defects of ptc2ptc3D or cdc5-ad.  Transient accumulation of Pds1 in the vaucole is also seen in wild type cells lacking PEP4 after induction of a DSB.  Unlike other adaptation-defective mutations, G2/M arrest persists even as the DNA damage-dependent phosphorylation of Rad53 diminishes, suggesting that cells have become unable to activate separase to initiate anaphase after DNA damage.  In addition, we have found that cells fail to recover when VPS51 is deleted or when ATG13-8SA is overexpressed.

Increased autophagy causes the delocalization of both Pds1 (securin) and Esp1 (separase) from the nucleus in checkpoint-arrested budding yeast cells. A. GFP-tagged Pds1 and Esp1 localize to the nucleus at the neck of G2/M-arrested wild type (WT) cells that have suffered a single unrepaired chromosome double-strand break (DSB). Both rdh54Δ and vps51Δ prevent cells from adapting and resuming cell cycle progression, but only ablating Vps51 – part of the Golgi-associated retrograde protein (GARP) complex – causes the mislocalization of Pds1 and Esp1 and the partial degradation of Pds1 by vacuolar proteases. Preventing degradation of Pds1 (and possibly other mitotic regulators) results in the suppression of permanent arrest and the relocalization of sufficient Esp1 into the nucleus to release cells from their pre-anaphase arrest. A similar suppression of arrest in vps51Δ cells is obtained by disabling autophagy (not shown). B. Induction of autophagy by overexpression of ATG13-8SA (6) prevents adaptation in wild type cells. Expression of ATG13-SA was induced at the same time that a single, unrepairable DSB was created. Whereas normal cells adapt by 24 h, increased autophagy prevents cells from progressing beyond the G2/M stage of the cell cycle. Deletion of the PEP4 gene that activates vacuolar proteases or ATG1 that is required for autophagy suppresses the arrest and allows cells to divide and resume cell cycle progression.

Taken together with other recent results (4, 5), these observations emphasize that the DNA damage response can trigger the mislocalisation and cytoplasmic proteolysis of important nuclear proteins that regulate DNA repair and cell cycle progression. These results broaden our perspective on the ways in which cells respond to DNA damage and delay cell cycle progression while such damage persists.

Ex MCB grad Farokh Dotiwala, current MCB grad Vinay Eapen and ex-postdoc Jake Harrison were the co-first authors on this paper. Assistant professor Satoshi Yoshida also contributed significantly to this project.

Dotiwala F(*), Eapen VV(*), Harrison JC(*), Arbel-Eden A, Ranade V, Yoshida S & Haber JE (2012) DNA damage checkpoint triggers autophagy to regulate the initiation of anaphase, PNAS (Published online before print November 19, 2012, doi: 10.1073/pnas.1218065109)

1.         Harrison JC & Haber JE (2006) Surviving the breakup: the DNA damage checkpoint. Annu Rev Genet 40:209-235.
2.         Dotiwala F, Haase J, Arbel-Eden A, Bloom K, & Haber JE (2007) The yeast DNA damage checkpoint proteins control a cytoplasmic response to DNA damage. Proc Natl Acad Sci U S A 104(27):11358-11363.
3.         Smolka MB, et al. (2006) An FHA domain-mediated protein interaction network of Rad53 reveals its role in polarized cell growth. J Cell Biol 175(5):743-753.
4.         Robert T, et al. (2011) HDACs link the DNA damage response, processing of double-strand breaks and autophagy. Nature 471(7336):74-79.
5.         Dyavaiah M, Rooney JP, Chittur SV, Lin Q, & Begley TJ (2011) Autophagy-dependent regulation of the DNA damage response protein ribonucleotide reductase 1. Mol Cancer Res 9(4):462-475.
6.         Kamada Y (2010) Prime-numbered Atg proteins act at the primary step in autophagy: unphosphorylatable Atg13 can induce autophagy without TOR inactivation. Autophagy 6(3):415-416.

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